5LM7 | pdb_00005lm7

Crystal structure of the lambda N-Nus factor complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth C]	SCOP2B Superfamily	Rad51 N-terminal domain-like	8040765	3000529	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rad51 N-terminal domain-like	8040765	3000529	SCOP2B (2022-06-29)
H [auth E]	SCOP2B Superfamily	Ribosomal protein S10	8102681	3001336	SCOP2B (2022-06-29)
C [auth J]	SCOP2B Superfamily	Ribosomal protein S10	8102681	3001336	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NusB-like	8038005	3000679	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	NusB-like	8038005	3000679	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth C]	S1_3	e5lm7C3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_3	ECOD (1.6)
F [auth C]	HHH_5	e5lm7C5	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
F [auth C]	KH_5	e5lm7C1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_5	ECOD (1.6)
F [auth C]	nusA	e5lm7C4	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: nusA	ECOD (1.6)
F [auth C]	NusA_N	e5lm7C2	A: a+b complex topology	X: Transcription factor NusA, N-terminal domain (From Topology)	H: Transcription factor NusA, N-terminal domain (From Topology)	T: Transcription factor NusA, N-terminal domain	F: NusA_N	ECOD (1.6)
A	S1_3	e5lm7A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_3	ECOD (1.6)
A	HHH_5	e5lm7A4	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
A	KH_5	e5lm7A3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_5	ECOD (1.6)
A	nusA	e5lm7A5	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: nusA	ECOD (1.6)
A	NusA_N	e5lm7A2	A: a+b complex topology	X: Transcription factor NusA, N-terminal domain (From Topology)	H: Transcription factor NusA, N-terminal domain (From Topology)	T: Transcription factor NusA, N-terminal domain	F: NusA_N	ECOD (1.6)
H [auth E]	Ribosomal_S10	e5lm7E1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein S10 (From Topology)	T: Ribosomal protein S10	F: Ribosomal_S10	ECOD (1.6)
C [auth J]	Ribosomal_S10	e5lm7J1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein S10 (From Topology)	T: Ribosomal protein S10	F: Ribosomal_S10	ECOD (1.6)
B	NusB	e5lm7B1	A: alpha complex topology	X: NusB-like (From Topology)	H: NusB-like (From Topology)	T: NusB-like	F: NusB	ECOD (1.6)
G [auth D]	NusB	e5lm7D1	A: alpha complex topology	X: NusB-like (From Topology)	H: NusB-like (From Topology)	T: NusB-like	F: NusB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth C]	3.30.1480.10	Alpha Beta	2-Layer Sandwich	N Utilization Substance Protein A	Chain:P	CATH (utative)
F [auth C]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (utative)
F [auth C]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
A	3.30.1480.10	Alpha Beta	2-Layer Sandwich	N Utilization Substance Protein A	Chain:P	CATH (utative)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (utative)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
H [auth E]	3.30.70.600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribosomal protein S10	CATH (4.3.0)
C [auth J]	3.30.70.600	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribosomal protein S10	CATH (4.3.0)
B	1.10.940.10	Mainly Alpha	Orthogonal Bundle	N-utilizing Substance Protein B Homolog	Chain A	CATH (4.3.0)
G [auth D]	1.10.940.10	Mainly Alpha	Orthogonal Bundle	N-utilizing Substance Protein B Homolog	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F [auth C]	PF13184	NusA-like first KH domain (KH_NusA_1st)	NusA-like first KH domain	This entry represents the first K homology (KH) domain found in NusA transcription termination factors. KH domains bind RNA and can function in RNA recognition [1]. NusA binds to RNA polymerase alpha subunit and promotes termination at certain RNA ha ...	This entry represents the first K homology (KH) domain found in NusA transcription termination factors. KH domains bind RNA and can function in RNA recognition [1]. NusA binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures [2]. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology (KH), KH1 and KH2. The KH domains of NusA belong to the type II KH RNA-binding domain superfamily [3].	Domain
A, F [auth C]	PF08529	NusA N-terminal domain (NusA_N)	NusA N-terminal domain	This domain represents the RNA polymerase binding domain of NusA.	Domain
A, F [auth C]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
C [auth J], H [auth E]	PF00338	Ribosomal protein S10p/S20e (Ribosomal_S10)	Ribosomal protein S10p/S20e	This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.	Domain
D [auth N], I [auth F]	PF11438	36-mer N-terminal peptide of the N protein (N36) (N36)	36-mer N-terminal peptide of the N protein (N36)	-	Family
B, G [auth D]	PF01029	NusB family (NusB)	NusB family	The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, F [auth C]	Transcription termination/antitermination protein NusA	protein binding binding protein domain specific binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA polymerase binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding transcription regulator activity DNA-binding transcription factor activity RNA binding protein binding binding protein domain specific binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA polymerase binding bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding enzyme binding transcription regulator activity DNA-binding transcription factor activity RNA binding nucleic acid binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process ribosome biogenesis ribonucleoprotein complex biogenesis regulation of DNA-templated transcription elongation DNA-templated transcription elongation	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol
C [auth J], H [auth E]	30S ribosomal protein S10	transcription antitermination factor activity, RNA binding transcription regulator activity RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process translation protein biosynthetic process cytoplasmic translation protein metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis regulation of DNA-templated transcription elongation DNA-templated transcription elongation	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome membrane-bounded organelle transcription elongation factor complex nucleus protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cytoplasm cytosol cytosolic small ribosomal subunit cytosolic ribosome
E [auth R], J [auth G]	RNA (29-MER)	-	-	-
D [auth N], I [auth F]	Antitermination protein N	DNA binding binding nucleic acid binding RNA binding single-stranded RNA binding RNA stem-loop binding RNA polymerase binding protein binding enzyme binding transcription antitermination factor activity, RNA binding transcription regulator activity bacterial-type RNA polymerase core enzyme binding RNA polymerase core enzyme binding	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation DNA-templated transcription elongation	-
B, G [auth D]	N utilization substance protein B homolog	RNA binding binding nucleic acid binding	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth C]	IPR036555	NusA, N-terminal domain superfamily	Homologous Superfamily
A, F [auth C]	IPR003029	S1 domain	Domain
A, F [auth C]	IPR013735	Transcription factor NusA, N-terminal	Domain
A, F [auth C]	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
A, F [auth C]	IPR010214	Transcription termination factor NusA, C-terminal duplication	Repeat
A, F [auth C]	IPR010213	Transcription factor NusA	Domain
A, F [auth C]	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
A, F [auth C]	IPR025249	Transcription factor NusA, first KH domain	Domain
A, F [auth C]	IPR030842	Transcription factor NusA, prokaryotes	Family
A, F [auth C]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, F [auth C]	IPR010995	DNA repair Rad51/transcription factor NusA, alpha-helical	Homologous Superfamily
C [auth J], H [auth E]	IPR027486	Small ribosomal subunit protein uS10 domain	Domain
C [auth J], H [auth E]	IPR036838	Small ribosomal subunit protein uS10 domain superfamily	Homologous Superfamily
C [auth J], H [auth E]	IPR018268	Small ribosomal subunit protein uS10, conserved site	Conserved Site
C [auth J], H [auth E]	IPR001848	Small ribosomal subunit protein uS10	Family
D [auth N], I [auth F]	IPR020952	Antitermination protein N, arginine-rich motif	Family
B, G [auth D]	IPR035926	NusB-like superfamily	Homologous Superfamily
B, G [auth D]	IPR011605	NusB antitermination factor	Family
B, G [auth D]	IPR006027	NusB/RsmB/TIM44	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.